Re: [PyMOL] APBS

Dear Robert,

Thank you for your note. You were right. I downloaded i386 for my Linux
computer and it runs. The funny part is that my computer has 64 bit
Xeon processor.
Go figure ...

Vaheh Oganesyan

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]On Behalf Of Robert
Campbell
Sent: Wednesday, May 30, 2007 11:06 AM
To: pym...@li...
Subject: Re: [PyMOL] APBS

Hi Vaheh,

* Oganesyan, Vaheh <Oga...@Me...> [2007-05-30 09:45] wrote:
> I did not get much luck with those recommendations either. I was doing
exactly the same. Something is phishy with my pymol and/or APBS
installation. I did check for different pdb files, so it is not pdb
related. The roor message is below:
>
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs',
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
> OSError Exception in Tk callback
>   Function: <function <lambda> at 0xf608448c> (type: <type
'function'>)
>   Args: ()
> Traceback (innermost last):
>   File
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.
py", line 1747, in __call__
>     return apply(self.func, args)
>   File
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py", line 153, in <lambda>
>     command=3Dlambda self=3Dself, name=3Dname: self._doCommand(name))
>   File
"/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py", line 132, in _doCommand
>     return command(name)
>   File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line
1101, in execute
>     (retval,progout) =3D
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),
))
>   File "/usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py", line
317, in run
>     retcode =3D
subprocess.call(args,stdout=3Doutput_file.fileno(),stderr=3Dsubprocess.ST=
DOU
T)
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 412, in
call
>     return Popen(*args, **kwargs).wait()
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 542, in
__init__
>     errread, errwrite)
>   File "/usr/bin/pymol/ext/lib/python2.4/subprocess.py", line 975, in
_execute_child
>     raise child_exception
> OSError: [Errno 8] Exec format error

                     ^^^^^^^^^^^^^^^^^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>
http://pldserver1.biochem.queensu.ca/~rlc

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